Keep an eye on it. See if it gets deeper. Are you digging in with your heels when you run?
I haven't been going barefoot much since about a month ago when it got too cold for shorts, and I broke out my selection of dress clothes, which never look good with bare feet, so I also broke out my dress shoes. This started happening a few weeks after my "barefoot season" ended. Also, I don't run, I'm not that athletic. So my guess was that this may have been damage done while going barefoot, and when I stopped, the skin sloughed off. But I wasn't sure.
I alternate between barefoot in late spring, summer, early fall, then dress shoes for the rest of the time. Now wearing dress shoes is my personal choice. I like the way they look on me, and they're not all that uncomfortable, actually. Plus, the line of work I'm currently in college for will require dress shoes.
Basically, here's how I do it, let's take one calendar year starting on January first: I kind of base it on season, but also on temperature zones. At the start of the year, which in Idaho is in the middle of winter, I'm wearing my winter leather dress boots. That lasts until temperatures rise, and it's consistently no lower than 40ºF(early spring), which is when i put away the boots and wear my dress sandals (with socks of course, as mens dress sandals don't look good without socks) until temperatures consistently stay above 60ºF (mid to late spring, and all of summer), I put away all shoes and go barefoot, even in the rain, as temperatures are beginning to warm up. I remain barefoot until temperatures start to get lower than 55ºF, and never get higher than 70ºF (early fall), then I go to my polished dress shoes until the snow starts to pile up, then I break out the boots, then the cycle starts again. Basically, when I can't wear shorts without freezing, that's when barefoot season ends. I define barefoot season as the Times of the year I can go barefoot outside, and go barefoot 24/7. The rest of the year, I may occasionally go barefoot outside, but it's rare. I even wear slippers indoors during the barefoot off season.